Added adjacent code

.github/workflows/check-reproducibility.yml

@@ -0,0 +1,48 @@
+name: Run Reproducibility Check
+on: [push, pull_request]
+jobs:
+  test:
+    strategy:
+      matrix:
+        maven: [ '3.9.2' ]
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+    - uses: actions/setup-java@v3
+      with:
+        distribution: 'zulu'
+        java-version: 17
+    - run: echo "JAVA17_HOME=$JAVA_HOME" >> $GITHUB_ENV
+    - run: java -version
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.12'
+    - name: Setup miniconda
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        python-version: 3.12
+        auto-update-conda: true
+        mamba-version: "*"
+        channels: conda-forge,defaults
+        activate-environment: AST
+        environment-file: environment.yml
+    - name: Install maven
+      uses: s4u/[email protected]
+      with:
+        java-version: 17
+        maven-version: ${{ matrix.maven }}
+    - name: Clean caches & workspace
+      run: make clean
+    - run: echo "LOGURU_COLORIZE=NO" >> $GITHUB_ENV
+    - name: Run small test
+      run: |
+        git config --global user.email "[email protected]"
+        git config --global user.name "Example Example"
+        head -n 101 results/combined/result.csv > results/combined/result_trimmed.csv
+        make check-merges-reproducibility
+      env:
+          GITHUB_TOKEN: ${{ secrets.TOKEN_GITHUB }}

.github/workflows/small-test.yml

@@ -29,8 +29,6 @@ jobs:
     - run: echo "JAVA17_HOME=$JAVA_HOME" >> $GITHUB_ENV
     - run: java -version
     - uses: actions/checkout@v4
-      with:
-        submodules: 'true'
     - name: Set up Python 3.8
       uses: actions/setup-python@v5
       with:

gitmerge_ort_imports.sh

@@ -0,0 +1,28 @@
+#!/usr/bin/env sh
+
+# usage: ./gitmerge_ort_imports.sh <clone_dir> <branch-1> <branch-2>
+
+clone_dir=$1
+branch1=$2
+branch2=$3
+
+export JAVA_HOME="$JAVA17_HOME"
+
+cd "$clone_dir" || exit 1
+
+git checkout "$branch1" --force
+
+attributes_file=".git/info/attributes"
+echo "*.java merge=merge-java" >> "$attributes_file"
+git config --local merge.merge-java.name "Merge Java files"
+git config --local merge.merge-java.driver 'java-merge-driver.sh "%A" "%O" "%B"'
+
+git merge --no-edit "$branch2"
+retVal=$?
+
+# report conflicts
+if [ "$retVal" -ne 0 ]; then
+    echo "Conflict"
+fi
+
+exit "$retVal"

run.sh

@@ -63,6 +63,9 @@ PATH=$(pwd)/src/scripts/merge_tools/:$PATH
 PATH=$(pwd)/src/scripts/merge_tools/merging/src/main/sh/:$PATH
 export PATH
 
+# Clone all submodules
+git submodule update --init --recursive
+
 # Check if cache.tar exists and cache is missing
 if [ -f cache.tar ] && [ ! -d cache ]; then
     echo "Decompressing cache.tar"

src/scripts/merge_tools/README

@@ -1,4 +1 @@
 git-hires-merge is from https://github.com/paulaltin/git-hires-merge .
-
-resolve-adjacent-conflicts, resolve-conflicts.py, and resolve-import-conflicts
-are from https://github.com/plume-lib/manage-git-branches .

src/scripts/merge_tools/gitmerge_ort_adjacent.sh

@@ -1,20 +1,28 @@
 #!/usr/bin/env sh
 
-# usage: ./gitmerge_ort_adjacent.sh <clone_dir> <branch-1> <branch-2>
+# usage: ./gitmerge_ort_imports.sh <clone_dir> <branch-1> <branch-2>
 
-MERGE_SCRIPTS_DIR="$(cd "$(dirname "$0")" && pwd -P)"
 clone_dir=$1
 branch1=$2
 branch2=$3
-strategy="-s ort"
-if "$MERGE_SCRIPTS_DIR"/gitmerge.sh "$clone_dir" "$branch1" "$branch2" "$strategy"; then
-  exit 0
-fi
+
+export JAVA_HOME="$JAVA17_HOME"
 
 cd "$clone_dir" || exit 1
-if ! "$MERGE_SCRIPTS_DIR"/resolve-adjacent-conflicts; then
-  echo "Conflict"
-  exit 1
+
+git checkout "$branch1" --force
+
+attributes_file=".git/info/attributes"
+echo "*.java merge=merge-java" >> "$attributes_file"
+git config --local merge.merge-java.name "Merge Java files"
+git config --local merge.merge-java.driver 'java-merge-driver.sh "%A" "%O" "%B" --only-adjacent'
+
+git merge --no-edit "$branch2"
+retVal=$?
+
+# report conflicts
+if [ "$retVal" -ne 0 ]; then
+    echo "Conflict"
 fi
 
-exit 0
+exit "$retVal"

src/scripts/merge_tools/gitmerge_ort_imports.sh

@@ -2,27 +2,19 @@
 
 # usage: ./gitmerge_ort_imports.sh <clone_dir> <branch-1> <branch-2>
 
+MERGE_SCRIPTS_DIR="$(cd "$(dirname "$0")" && pwd -P)"
 clone_dir=$1
 branch1=$2
 branch2=$3
-
-export JAVA_HOME="$JAVA17_HOME"
+strategy="-s ort"
+if "$MERGE_SCRIPTS_DIR"/gitmerge.sh "$clone_dir" "$branch1" "$branch2" "$strategy"; then
+  exit 0
+fi
 
 cd "$clone_dir" || exit 1
-
-git checkout "$branch1" --force
-
-attributes_file=".git/info/attributes"
-echo "*.java merge=merge-java" >> "$attributes_file"
-git config --local merge.merge-java.name "Merge Java files"
-git config --local merge.merge-java.driver 'java-merge-driver.sh "%A" "%O" "%B"'
-
-git merge --no-edit "$branch2"
-retVal=$?
-
-# report conflicts
-if [ "$retVal" -ne 0 ]; then
-    echo "Conflict"
+if ! "$MERGE_SCRIPTS_DIR"/resolve-import-conflicts; then
+  echo "Conflict"
+  exit 1
 fi
 
-exit "$retVal"
+exit 0

src/scripts/merge_tools/gitmerge_ort_imports_ignorespace.sh

@@ -1,29 +1,20 @@
 #!/usr/bin/env sh
 
-# usage: ./gitmerge_ort_imports_ingorespace.sh <clone_dir> <branch-1> <branch-2>
+# usage: ./gitmerge_ort_imports_ignorespace.sh <clone_dir> <branch-1> <branch-2>
 
+MERGE_SCRIPTS_DIR="$(cd "$(dirname "$0")" && pwd -P)"
 clone_dir=$1
 branch1=$2
 branch2=$3
-strategy="-Xignore-space-change"
-
-export JAVA_HOME="$JAVA17_HOME"
+strategy="-s ort -Xignore-space-change"
+if "$MERGE_SCRIPTS_DIR"/gitmerge.sh "$clone_dir" "$branch1" "$branch2" "$strategy"; then
+  exit 0
+fi
 
 cd "$clone_dir" || exit 1
-
-git checkout "$branch1" --force
-
-attributes_file=".git/info/attributes"
-echo "*.java merge=merge-java" >> "$attributes_file"
-git config --local merge.merge-java.name "Merge Java files"
-git config --local merge.merge-java.driver 'java-merge-driver.sh "%A" "%O" "%B"'
-
-git merge --no-edit "$strategy" "$branch2"
-retVal=$?
-
-# report conflicts
-if [ "$retVal" -ne 0 ]; then
-    echo "Conflict"
+if ! "$MERGE_SCRIPTS_DIR"/resolve-import-conflicts; then
+  echo "Conflict"
+  exit 1
 fi
 
-exit "$retVal"
+exit 0

src/scripts/merge_tools/resolve-import-conflicts

@@ -0,0 +1,39 @@
+#!/bin/bash
+# bash, not POSIX sh, because of "readarray".
+
+# This script edits files in place to remove conflict markers related to Java
+# imports.  For a given conflict that involves only `import` statements and
+# blank lines, the output includes every `import` statement that is in either
+# of the parents.  This script leaves other conflicts untouched.
+
+# Usage:
+#   resolve-import-conflicts [file ...]
+#
+# The script works on all files given on the command line.
+# If none are given, the script works on all files in or under the current directory.
+#
+# The exit status code is 0 (success) if all conflicts are resolved in all the files.
+# The exit status code is 1 (failure) if any conflict remains.
+
+# This script is not a git mergetool.  A git mergetool is given the base, parent 1, and
+# parent 2 files, all without conflict markers.
+# However, this can be run after a git mergetool that leaves conflict markers
+# in files, as the default git mergetool does.
+
+if [ "$#" -eq 0 ] ; then
+  readarray -t files < <(grep -l -r '^<<<<<<< HEAD' .)
+else
+  files=("$@")
+fi
+
+SCRIPTDIR="$(cd "$(dirname "$0")" && pwd -P)"
+
+status=0
+
+for file in "${files[@]}" ; do
+  if ! "${SCRIPTDIR}"/resolve-conflicts.py --java_imports "$file" ; then
+    status=1
+  fi
+done
+
+exit $status